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- PDB-6tnm: E. coli aerobic trifunctional enzyme subunit-alpha -

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Basic information

Entry
Database: PDB / ID: 6tnm
TitleE. coli aerobic trifunctional enzyme subunit-alpha
ComponentsFatty acid oxidation complex subunit alphaBeta oxidation
KeywordsOXIDOREDUCTASE / fatty acid oxidation / lipid metabolism / hydratase / dehydrogenase / trifunctional enzyme / beta oxidation
Function / homology
Function and homology information


fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity ...fatty acid beta-oxidation multienzyme complex / 3-hydroxybutyryl-CoA epimerase / 3-hydroxybutyryl-CoA epimerase activity / Delta3-Delta2-enoyl-CoA isomerase / delta(3)-delta(2)-enoyl-CoA isomerase activity / long-chain-3-hydroxyacyl-CoA dehydrogenase activity / 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase activity / enoyl-CoA hydratase activity / fatty acid beta-oxidation / NAD+ binding
Similarity search - Function
Fatty oxidation complex, alpha subunit FadB / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. ...Fatty oxidation complex, alpha subunit FadB / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 - #50 / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / ClpP/crotonase-like domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / NITRATE ION / Fatty acid oxidation complex subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSah-Teli, S.K. / Hynonen, M.J. / Wierenga, R.K. / Venkatesan, R.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland289024, 293369, 319194 Finland
Citation
Journal: J.Struct.Biol. / Year: 2020
Title: Insights into the stability and substrate specificity of the E. coli aerobic beta-oxidation trifunctional enzyme complex.
Authors: Sah-Teli, S.K. / Hynonen, M.J. / Sulu, R. / Dalwani, S. / Schmitz, W. / Wierenga, R.K. / Venkatesan, R.
#1: Journal: Biochem J / Year: 2019
Title: Complementary substrate specificity and distinct quaternary assembly of the aerobic and anaerobic β-oxidation trifunctional enzyme complexes.
Authors: Shiv K Sah-Teli / Mikko J Hynönen / Werner Schmitz / James A Geraets / Jani Seitsonen / Jan Skov Pedersen / Sarah J Butcher / Rik K Wierenga / Rajaram Venkatesan /
Abstract: The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, ...The trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in , EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, whereas anEcTFE is expressed also under anaerobic conditions, with nitrate or fumarate as the ultimate electron acceptor. The anEcTFE subunits have higher sequence identity with the human mitochondrial TFE (HsTFE) than with the soluble EcTFE. Like HsTFE, here it is found that anEcTFE is a membrane-bound complex. Systematic enzyme kinetic studies show that anEcTFE has a preference for medium- and long-chain enoyl-CoAs, similar to HsTFE, whereas EcTFE prefers short chain enoyl-CoA substrates. The biophysical characterization of anEcTFE and EcTFE shows that EcTFE is heterotetrameric, whereas anEcTFE is purified as a complex of two heterotetrameric units, like HsTFE. The tetrameric assembly of anEcTFE resembles the HsTFE tetramer, although the arrangement of the two anEcTFE tetramers in the octamer is different from the HsTFE octamer. These studies demonstrate that EcTFE and anEcTFE have complementary substrate specificities, allowing for complete degradation of long-chain enoyl-CoAs under aerobic conditions. The new data agree with the notion that anEcTFE and HsTFE are evolutionary closely related, whereas EcTFE belongs to a separate subfamily.
History
DepositionDec 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1May 20, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fatty acid oxidation complex subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,34210
Polymers81,3081
Non-polymers1,0339
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint3 kcal/mol
Surface area30230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.384, 214.113, 76.520
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Fatty acid oxidation complex subunit alpha / Beta oxidation


Mass: 81308.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: fadB, oldB, b3846, JW3822 / Variant: MG1655 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P21177, enoyl-CoA hydratase, 3-hydroxybutyryl-CoA epimerase, Delta3-Delta2-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63 % / Description: rod shape, long, branched, cluster
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Bis-Tris propane, pH 7.5, 25% w/v PEG 3550, 367 mM KNO3 and 25 mM ATP
PH range: 7.2-7.6 / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: frozen in liquid nitrogen / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 21, 2018
RadiationMonochromator: Double crystal 28.290m / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.949→65.19 Å / Num. obs: 23039 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 56.85 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.108 / Net I/σ(I): 5.9
Reflection shellResolution: 2.949→3.13 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3661 / CC1/2: 0.439 / Rpim(I) all: 0.415 / % possible all: 99.9

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Processing

Software
NameVersionClassification
xia22data reduction
DIALS1.14data scaling
MoRDaphasing
PHENIX1.16_3549refinement
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1wdk-chainA

1wdk


Resolution: 2.95→53.53 Å / SU ML: 0.4246 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 29.6929
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2711 1082 4.71 %
Rwork0.23 21911 -
obs0.2318 22993 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.76 Å2
Refinement stepCycle: LAST / Resolution: 2.95→53.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 0 65 32 5627
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00235712
X-RAY DIFFRACTIONf_angle_d0.59867732
X-RAY DIFFRACTIONf_chiral_restr0.0412859
X-RAY DIFFRACTIONf_plane_restr0.0041999
X-RAY DIFFRACTIONf_dihedral_angle_d18.03733443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.080.39361440.35232673X-RAY DIFFRACTION99.79
3.08-3.250.36251390.33122689X-RAY DIFFRACTION99.65
3.25-3.450.35851360.31542697X-RAY DIFFRACTION99.89
3.45-3.720.29861530.26952692X-RAY DIFFRACTION99.96
3.72-4.090.28891380.23122733X-RAY DIFFRACTION99.9
4.09-4.680.22641090.17572760X-RAY DIFFRACTION99.97
4.68-5.90.21021340.19012779X-RAY DIFFRACTION100
5.9-53.530.19851290.17892888X-RAY DIFFRACTION99.64
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9609292530450.05757806633590.1488901494031.53075834118-0.6468908498582.18393928285-0.04480826366030.01589638308870.0391685651910.217265926674-0.0697917425649-0.257817423962-0.3923511877130.5757252263380.06318736719820.372576411765-0.0593992736918-0.006373953911880.3682370891060.000813650361630.2125814219443.890528201752.5644891986-7.46736072884
20.586036122585-0.441942038555-0.6476774410391.158948500280.836997648221.068826436160.07712013918550.0536885535993-0.2069596371550.120494973710.405446324642-0.712294163931-0.04711537691880.392904125909-0.1191565721830.293247660385-0.00346523886353-0.1388123066410.500228147076-0.2628173381240.75685493353744.655817440512.6661264818-22.531263931
32.306932386610.2034182447170.280060796182.015369226050.623428400652.204782547520.1596001619820.538133736374-0.349374525845-0.303974450251-0.0138555453240.1069720305130.0764512328518-0.116572010067-0.08552832164990.3274163896160.0278556787574-0.05770358853570.43183500454-0.1348871995360.37280529544818.616279499818.2231248505-28.6106225707
41.98830933934-0.175763684194-0.5495574894631.68794607772-0.2443895589691.840220705380.193894541844-0.2088025013790.01939222268230.328895821507-0.06896564995290.0502004890348-0.014422449311-0.34358486429-0.0328892984630.316600329289-0.0887997327688-0.08274035459790.306887202916-0.1006452373780.36377037580718.889814163922.651698085-8.40641996771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 283 )
2X-RAY DIFFRACTION2chain 'A' and (resid 284 through 483 )
3X-RAY DIFFRACTION3chain 'A' and (resid 484 through 644 )
4X-RAY DIFFRACTION4chain 'A' and (resid 645 through 719 )

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